I'm glad that your son on his way to complete recovery, hopefully he is doing well! Only thing I would watch for are doses of vitamin C over 2 mg, they seem to deplete copper rather fast.
My story is very similiar altough instead of Antibiotics I wiped out "good bugs" by zinc overdosing - taking more 100 mg zinc a day for more than half a year. Copper is well known mineral for regulating fungus and yeast (in right doses) so by overdosing on zinc I believe that I completely slaughtered all the good microflora. It"s just a few days since I discovered that histamine/undermethylation issuse may be "final puzzle" of my recovery and if I get this correct, hopefully I will recover completely.
Obivously way out of this is to introduce quality probiotic, but what to do with issue of histamine? I can barefuly function if I take probiotic. Have you find way, for your son to tolerate probiotics?